2015 : Protein Structure Hub

Publications

  1. Asano N., Kato K., Nakamura A., Komoda K., Tanaka I., Yao M.
    Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis
    Nucl. Acid Res. 43, 4746-4757 (2015)
  2. Shen X., Saburi W., Gai Z., Kato K., Ojima-Kato T., Yu J., Komoda K., Kido Y., Matsui H., Mori H., Yao M.
    Structural analysis of the alpha-glucosidase HaG provides new insights into substrate specificity and catalytic mechanism
    Acta Cryst. D. 71, 1382-1391 (2015)
  3. Gai Z., Matsuno A., Kato K., Kato S., Khan Md-Rafiqul-Islam., Shimizu T., Yoshioka T., Kato Y., Kishimura H., Kanno G., Miyabe Y., Terada T., Tanaka Y., Yao M.
    Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 Angstrom Resolution
    Structure 23, 2204-2212 (2015)
  4. Kumagai Y., Yamashita K., Tagami T., Uraji M., Wan K., Okuyama M., Yao M., Kimura A., Hatanaka T.
    The loop structure of Actinomycete glycoside hydrolase family 5 mannanases governs substrate recognition
    FEBS J. 282, 4001-4014 (2015)
  5. Matsuno A., Gai Z., Tanaka M., Kato K., Kato S., Katoh T., Shimizu T., Yoshioka T., Kishimura H., Tanaka Y., Yao M.
    Crystallization and preliminary X-ray crystallographic study of a 3.8-MDa respiratory supermolecule hemocyanin
    J. Struct. Biol. 190, 379-382 (2015)
  6. Sugawara T., Yamashita D., Kato K., Peng Z., Ueda J., Kaneko J., Kamio Y., Tanaka Y., Yao M.
    Structural basis for pore-forming mechanism of staphylococcal alpha-hemolysin
    Toxicon 108, 226-231 (2015)
  7. Uchida T., Sasaki M., Tanaka Y., Ishimori K.
    A Dye-Decolorizing Peroxidase from Vibrio cholerae
    Biochemistry 54, 6610-6621 (2015)
  8. Sasaki R., Kitazawa S., Kitahara R., Nakazawa H., Tanaka Y., Kumagai I., Umetsu M., Makabe K.
    Zinc Ion-binding Activity of an Anti-ZnO VHH Antibody, 4F2
    Chem. Letters 44, 1309-1311 (2015)
  9. Ose T., Oikawa A., Nakamura Y., Maenaka K., Higuchi Y., Satoh Y., Fujiwara S., Demura M., Sone T., Kamiya M.
    Solution structure of an avirulence protein, AVRPia, from Magnaporthe oryzae.
    Journal of Biomolecular NMR. 63, 229-235 (2015)
  10. Furuse M., Tamogami J., Hosaka T., Kikukawa T., Shinya N., Hato N., Ohsawa N., S. Y. Kim, K.-H. Jung, Demura M., Miyauchi S., Kamo N., Shimono K., Kimura-Someya T., Yokoyama S., Shirouzu M.
    Structural Basis for Slow Photocycle and Late Proton Release in Acetabularia Rhodopsin I from the Marine Plant, Acetabularia acetabulum, and membrane potential-induced modulation of the
    photocycle.
    Acta Crystallographica Section D. 71, 2203-2216 (2015)
  11. Kikukawa T., Kusakabe C., Kokubo A., Tsukamoto T., Kamiya M., Aizawa T., Ihara K., Kamo N., Demura M.
    Probing the Cl–pumping photocycle of pharaonis halorhodopsin: Examinations with bacterioruberin, an intrinsic dye, and membrane potential-induced modulation of the photocycle.
    Biochim. Biophys. Acta – Bioenergetics. 1847, 748-758 (2015)
  12. Tomisawa S., Sato Y., Kamiya M., Kumaki Y., Kikukawa T., Kawano K., Demura M., Nakamura K., Ayabe T., Aizawa T.
    Efficient production of a correctly folded mouse a-defensin, cryptdin-4, by refolding during inclusion body solubilization.
    Protein Expression and Purification. 112, 21-28 (2015)
  13. Baek M., Kamiya M., Kushibiki T., Nakazumi T., Tomisawa S., Abe C., Kumaki T., Kikukawa T., Demura M., Kawano K., Aizawa T.
    Lipopolysaccharide-bound structure of the antimicrobial peptide cecropin P1 determined by nuclear magnetic resonance spectroscopy.
    Journal of Peptide Science. Accepted (2016)
  14. Md. Ruhul Kuddus, Farhana Rumi, Tsutsumi M., Takahashi R., Yamano M., Kamiya M., Kikukawa T., Demura M., Aizawa T.
    Expression, purification and characterization of the recombinant cysteine-rich antimicrobial peptide snakin-1 in Pichia pastoris.
    T. Protein Expression and Purification. 122, 15-22 (2016)
  15. Tamogami J., Sato K., Kurokawa S., Yamada T., Nara T., Demura M., Miyauchi S., Kikukawa T., Muneyuki E., Kamo N.
    Formation of M-Like Intermediates in Proteorhodopsin in Alkali Solutions (pH > 8.5) Where the Proton Release Occurs First in Contrast to the Sequence at Lower pH.
    N. Biochemistry. 55, 1036-1048 (2016)
  16. Tamaki H., Egawa A., Kido K., Kameda T., Kamiya M., Kikukawa T., AizawaT., Fujiwara T., Demura M.
    Structure determination of uniformly 13C, 15N labeled protein using qualitative distance restraints from MAS solid-state 13C-NMR observed paramagnetic relaxation enhancement.
    Journal of Biomolecular NMR. 64, 87-101 (2016)
  17. Hasemi T., Kikukawa T., Kamo N., Demura M.
    Characterization of a Cyanobacterial Chloride-Pumping Rhodopsin and Its Conversion into a Proton Pump.
    J. Biol. Chem. 291, 355-362 (2016)
  18. Yamamoto H., Shima T., Yamaguchi M., Mochizuki Y., Hoshida H., Kakuta S., Kondo-Kakuta C., Noda NN., Inagaki F., Itoh T., Akada R., Ohsumi Y.
    The Thermotolerant Yeast Kluyveromyces marxianus Is a Useful Organism for Structural and Biochemical Studies of Autophagy.
    J Biol Chem. 290, 29506-29518 (2015)
  19. Funami K., Matsumoto M., Enokizono Y., Ishii N., Tatematsu M., Oshiumi H., Inagaki F., Seya T.
    Identification of a Regulatory Acidic Motif as the Determinant of Membrane Localization of TICAM-2.
    J Immunol. 195, 4456-4465 (2015)
  20. Imai M., Saio T., Kumeta H., Uchida T., Inagaki F., Ishimori K.
    Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c.
    Biochem Biophys Res Commun. 469, 978-984 (2015)
  21. Saio T., Ogura K., Kumeta H., Kobashigawa Y., Shimizu K., Yokochi M., Kodama K., Yamaguchi H., Tsujishita H., Inagaki F.
    Ligand-driven conformational changes of MurD visualized by paramagnetic NMR.
    Sci Rep. 5, 16685 (2015)
  22. Kobashigawa Y., Amano S., Yokogawa M., Kumeta H., Morioka H., Inouye M., Schlessinger J., Inagaki F.
    Structural analysis of the mechanism of phosphorylation of a critical autoregulatory tyrosine residue in FGFR1 kinase domain.
    Genes Cells. 20, 860-870 (2015)
  23. Mazhab-Jafari MT., Marshall CB., Smith MJ., Gasmi-Seabrook GM., Stathopulos PB., Inagaki F., Kay LE., Neel BG., Ikura M.
    Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site.
    Proc Natl Acad Sci U S A. 112, 6625-6630 (2015)
  24. Yokogawa M., Tsushima T., Noda NN., Kumeta H., Enokizono Y., Yamashita K., Standley DM., Takeuchi O., Akira S., Inagaki F.
    Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions.
    Sci Rep. 6, 22324 (2016)

Books etc

  1. 姚閔、中澤祐人
    システイニルtRNAを合成するトランスサルファソームの分子基盤
    日本結晶学会誌 57(4), 245-249 (2015)
  2. 姚閔
    トランスサルファソーム、ネイティブ－ページ
    日本結晶学会誌 57(4), 255 (2015)
  3. Yamashita D., Sugawara T., Tanaka I., Tanaka Y., Yao M.
    Pore formation mechanism of staphylococcal pore forming toxin
    PF activity report part A, 2014 Highlight, 46-47 (2015)
  4. 田中勲
    タンパク質結晶学方法論の開発と網羅的解析（学会賞受賞論文）
    日本結晶学会誌 57(3), 155-162 (2015)
  5. 田中勲
    タンパク質の位相決定法、タンパク質の構造精密化、リボソーム
    日本結晶学会誌 57(3), 203-204 (2015)
  6. 田中良和
    黄色ブドウ球菌が産生する膜孔形成毒素の作用機構
    Isotope News 736, 7-11 (2015)
  7. 田中良和
    黄色ブドウ球菌の２成分性膜孔形成毒素γヘモリジンの膜孔形成メカニズム　失敗から明らかになった毒素の戦略
    化学と生物 53(3), 136-137 (2015)
  8. 出村誠
    光のエネルギー利用27　ハロロドプシン『光と生命の事典』（日本光生物学協会「光と生命の事典」編集委員会 編）
    朝倉書店 (2016)
  9. Kikukawa T., Kamo N., Demura M.
    Photochemistry of Halorhodopsin in Optogenetics
    (Eds. Hideki Kandori, Hiromu Yawo, Amane Koizumi)
    Springer., 47-62 (2016)

Conference Activities & Talks

(Invited talk)

  1. December 2015
    Kolkata, India
    The 13th Conference of the Asian Crystallographic Association (AsCA2015)
    Solution free crystal-mounting method for collecting high quality data using low energy X-ray
    Yao M.
  2. December 2015
    Royal Hawaiian (Hawaii)
    環太平洋化学会　Pacifichem 2015,
    Backbone structure determination of protein in solid state using paramagnetic relaxation enhancement and chemical shifts.
    Demura M.
  3. March 2016
    Busan, South Korea
    Hokkaido University / Pusan National University
    Joint Symposium 2016 in Busan
    Molecular mechanism of staphylococcal pore forming toxin
    Tanaka Y.

Invited talk (in Japan)

  1. 2015年6月
    徳島市
    第15回日本蛋白質科学会年会　ワークショップ　巨大生物マシンの構築原理と機能発現
    黄色ブドウ球菌が赤血球を破壊する毒素の作用原理（Molecular mechanism of pore forming toxin from Staphylococcus aureus）
    田中　良和
  2. 2015年9月
    岡崎市
    生理学研究所 研究会「膜システムの機能的・構造的統合」
    Ｘ線結晶構造解析により明らかになった黄色ブドウ球菌の膜孔形成毒素蛋白質の膜孔形成機構
    田中　良和
  3. 2015年10月
    東京都
    JST発　医療分野　新技術説明会　A-STEPから創出された最新シーズ技術を一挙公開
    ペプチド性タグを利用したタンパク質結晶化の新技術－タンパク質結晶構造解析のための実用的な結晶化タグ－
    姚　閔

Patent

  1. 2015/3/26（特許出願PCT/JP2015/059332）
    生物学的試料をハイドロゲルで高速固定する方法及びそのための装置
    発明者：田中勲、篠田晃、姚閔、田中良和